On Thu, Oct 29, 2015 at 7:21 PM, Alan <alanwilter.gmail.com> wrote:
> Dear Jason, I gave a try and it’s simply wonderful.
>
> However, I didn’t get the same E_pot_tot for the same system with U-B using
> sander x gmx.
>
> I took
>
> ---------------------------------
> cat << EOF >| mdin
> Single point
> &cntrl
> imin=0, maxcyc=0,
> ntmin=2,
> ntb=0,
> igb=0,
> cut=999,
> //
> EOF
>
> cat << EOF >| SPE.mdp
> define = -DFLEXIBLE
> integrator = md
> nsteps = 0
> dt = 0.001
> constraints = none
> emtol = 10.0
> emstep = 0.01
> nstcomm = 1
> ns_type = simple
> nstlist = 0
> rlist = 0
> rcoulomb = 0
> rvdw = 0
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> nstxout = 1
> pbc = no
> nstlog = 1
> nstenergy = 1
> nstvout = 1
> nstfout = 1
> nstxtcout = 1
> comm_mode = ANGULAR
> continuation = yes
> cutoff-scheme = group
> EOF
>
> cp $AMBERHOME/AmberTools/test/chamber/ala_ala_ala/inpcrd.save .
> cp $AMBERHOME/AmberTools/test/chamber/ala_ala_ala/prmtop.save .
>
> python2.7
> import parmed as pmd
> pmd.load_file('prmtop.save').save('gromacs.top')
> exit()
>
> # Gromacs 5.1
> gmx grompp -f SPE.mdp -c prmtop.pdb -p gromacs.top -o gromacs.tpr
> gmx mdrun -ntmpi 1 -v -deffnm gromacs
> echo 1 2 3 4 5 6 7 8 9 10 11 12| gmx energy -f gromacs.edr
> # EPot= 234.4 kJ/mol
>
> # AT15
> sander -O -i mdin -o mdout -p prmtop.save -c inpcrd.save
> mv mdinfo prmtop.mdinfo
> cat prmtop.mdinfo
> # EPot= 39.1266 kcal/mol x 4.184 = 163.7057 kJ/mol
>
​Do you know what component the energy differs in? It's possible that the
difference is in the 1-4 nonbondeds, since CHARMM doesn't have a uniform
scaling factor applied to all L-J interactions like the AMBER force field
does -- it assigns different L-J parameters for 1-4s. I know GROMACS
supports this (I actually have a test in ParmEd that goes GROMACS -> AMBER
using the CHARMM FF and get the same results in both programs).
If it's broken going the other way, it's something I have to look into.
Thanks,
Jason
​
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 29 2015 - 19:00:04 PDT
